PCAngsdTutorial

We will go through a simple and more complex example on how to use PCAngsd with visualization of the data.

PCA with admixture aware priors

This example will perform a PCA analysis on 1000 genotype likelihoods.

Set paths

Every time you open a new terminal window, set the paths to the program and the input file.

Set the path to PCAngsd

PCAngsd=~/Software/PCAngsd

Test the link

ls $PCAngsd

Create directories

Create the directories that will be used for working:

mkdir Demo

cd Demo

mkdir Data

mkdir Results

Set the paths to your local directories

IN_DIR=Demo/Data

OUT_DIR=Demo/Results

Test the links

ls $IN_DIR

ls $OUT_DIR

Download the beagle genotype likelihood input file

PCAngsd uses Genotype Likelihoods (GLs) in .beagle format as input. The input file has been created for you.

Download the files and move them to your input folder (for example, $IN_DIR):

*ANDERS*

wget popgen.dk/software/download/NGSadmix/data/Demo1input.gz

wget popgen.dk/software/download/NGSadmix/data/Demo1pop.info

mv Demo1input.gz $IN_DIR

mv Demo1pop.info $IN_DIR

*ANDERS*